Hi :
i face a relax problem, the error log is
Traceback (most recent call last):
File "./relax-Device-fr-relaxed-D3-five-layer-Au-fix-bottom-3layer-fr-relaxed-Au-111-by-vasp-fr-relaxed-Au-by-vasp-change-a-b-POSCAR-relaxed-by-liming.py", line 802, in <module>
optimizer_method=LBFGS(),
File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 331, in OptimizeGeometry
File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 467, in runSimultaneousRelaxation
File "./zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 376, in runRelaxation
File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 289, in get_forces
File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 164, in _update
File "./zipdir/NL/Calculators/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 34, in energyFunction
File "./zipdir/NL/Calculators/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 71, in _checkAndUpdate
File "./zipdir/NL/Calculators/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 107, in _update
File "./zipdir/NL/ComputerScienceUtilities/Timer.py", line 45, in __call__
File "./zipdir/NL/Calculators/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 106, in <lambda>
File "./zipdir/NL/Calculators/LCAOCalculator/Analysis/EnergyForcesStress.py", line 254, in calculateLCAOEnergyForcesStress
File "./zipdir/NL/Calculators/GenericParameters/GrimmeDFTD3.py", line 461, in _adjustStress
File "./zipdir/NL/Calculators/GenericParameters/GrimmeDFTD3.py", line 495, in _calculateCorrections
File "./zipdir/NL/Calculators/GenericParameters/GrimmeDFTD3.py", line 670, in __buildCPPObjects
UnboundLocalError: local variable 'periodicity' referenced before assignment
and at the end of output file, , there are information below, i don not konw whether the relax is complete or not, because there are words: Calculation Converged in 17 steps , does it meaming the relaxed is complete or not?
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3060 x 3060 [143 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| 213 Au [ 2.079 , 14.792 , 66.928 ] 10.98515 -0.01485 |
| 214 Au [ 0.840 , 9.714 , 66.939 ] 11.01089 0.01089 |
| 215 Au [ 4.116 , 12.264 , 66.939 ] 10.98587 -0.01413 |
| 216 Ti [ 0.859 , 18.756 , 67.452 ] 3.86359 -0.13641 |
| 217 S [ 3.337 , 19.732 , 67.456 ] 6.08704 0.08704 |
| 218 S [ 2.275 , 23.070 , 67.460 ] 5.98240 -0.01760 |
| 219 S [ 4.364 , 23.102 , 67.461 ] 5.99040 -0.00960 |
+------------------------------------------------------------------------------+
| 17 E = -503.204 dE = 9.084030e-05 dH = 3.281213e-05 |
+------------------------------------------------------------------------------+
| Calculation Converged in 17 steps |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Device DFT Calculation [Finished Mon Mar 7 16:30:18 2016] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3060 x 3060 [143 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of orbitals in real space is disabled. |
| Enabling storage requires an additional 1177 MB. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 502) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 882 x 882 [12 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of atomic core grids requires 10 MB per grid |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 882 x 882 [12 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of atomic core grids requires 10 MB per grid |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3060 x 3060 [143 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Size of dense matrices = 3060 x 3060 [143 MB per matrix] |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of atomic core grids requires 52 MB per grid |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of atomic core grids requires 10 MB per grid |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Real space grid sampling is (37, 374, 101) in a, b, and c directions. |
| |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| |
| Storage of atomic core grids requires 10 MB per grid |
| |
+------------------------------------------------------------------------------+
| Left electrode chemical potential = -4.019404 eV |
| Right electrode chemical potential = -4.019404 eV |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Density Matrix : ==================================================
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
Timing: Total Per Step %
--------------------------------------------------------------------------------
Diagonalization : 84569.99 s 1595.66 s 66.94% |=============|
Density Matrix : 26163.15 s 1453.51 s 20.71% |===|
Setting Density Matrix : 22052.99 s 7351.00 s 17.46% |===|
Exchange-Correlation : 1690.38 s 22.84 s 1.34% |
Real Space Integral : 599.67 s 8.10 s 0.47% |
Valence Density : 483.24 s 6.53 s 0.38% |
Hartree Potential : 212.15 s 2.87 s 0.17% |
Mixing : 17.42 s 0.25 s 0.01% |
Constant Terms : 15.87 s 7.93 s 0.01% |
Difference Density : 12.14 s 0.22 s 0.01% |
Real Space Basis : 9.70 s 3.23 s 0.01% |
Loading Modules + MPI : 3.95 s 3.95 s 0.00% |
Core Density : 3.66 s 0.07 s 0.00% |
Neutral Atom Potential : 3.41 s 1.70 s 0.00% |
Basis Set Generation : 2.30 s 0.77 s 0.00% |
File IO, nlsave : 0.24 s 0.24 s 0.00% |
Hubbard Term : 0.00 s 0.00 s 0.00% |
Fixed Spins Term : 0.00 s 0.00 s 0.00% |
--------------------------------------------------------------------------------
Total : 126329.92 s (1d11h05m29.92s)
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
